I upgraded everything. I don't think you'll get much benefit of putting new speakers only unless you get some very low power requirement speakers, like infinity reference for example.
I upgraded my head unit to a Kenwood DDX8019.

Then upgraded the front dash and rear pillar with 3.5" infinity reference, and the doors with 6x9 infinity reference. These are being powered by the new head unit, and they sound good, they would sound much better if I had purchased Infinity Kappas and amped them. Using those speakers (or similar low end speakers) with the factory head unit WILL provide some improvement, mostly in efficiency, they may prove to be a little more loud and clear, but you'll probably lose some bass.
I bought a sub from wickedcas

and placed the amp under the drivers seat (nav/tv/hdradio are under the passenger)
And... It rocks. I originally had the system without the wickedcas subwoofer and it was good with the factory subwoofer, but lacked any kind of serious low end below 80Hz. Upgrading the sub was a HUGE step.